Last data update: 2014.03.03

 R: High level constructors for DAVIDWebService package's...
DAVIDGenesR Documentation

High level constructors for DAVIDWebService package's classes.

Description

Different ways to build the different DAVIDWebService's object according to the signature in use.

Usage

  DAVIDGenes(object)

  ## S4 method for signature 'character'
DAVIDGenes(object)

  ## S4 method for signature 'data.frame'
DAVIDGenes(object)

  ## S4 method for signature 'DAVIDGenes'
initialize(.Object, fileName)

  as(object, Class, strict=TRUE,
  ext=possibleExtends(thisClass, Class))

  DAVIDFunctionalAnnotationChart(object)

  ## S4 method for signature 'character'
DAVIDFunctionalAnnotationChart(object)

  ## S4 method for signature 'data.frame'
DAVIDFunctionalAnnotationChart(object)

  ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
initialize(.Object,
  fileName)

  as(object, Class, strict=TRUE,
  ext=possibleExtends(thisClass, Class))

  ## S4 method for signature 'DAVIDCluster'
initialize(.Object, fileName)

  ## S4 method for signature 'DAVIDGeneCluster'
initialize(.Object,
  fileName)

  DAVIDGeneCluster(object)

  ## S4 method for signature 'character'
DAVIDGeneCluster(object)

  ## S4 method for signature 'DAVIDTermCluster'
initialize(.Object,
  fileName)

  DAVIDTermCluster(object)

  ## S4 method for signature 'character'
DAVIDTermCluster(object)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
initialize(.Object,
  fileName)

  as(object, Class, strict=TRUE,
  ext=possibleExtends(thisClass, Class))

  DAVIDFunctionalAnnotationTable(object)

  ## S4 method for signature 'character'
DAVIDFunctionalAnnotationTable(object)

  ## S4 method for signature 'data.frame'
DAVIDFunctionalAnnotationTable(object)

  ## S4 method for signature 'DAVIDGODag'
initialize(.Object,funChart,type=c("BP","MF","CC"),pvalueCutoff=0.1,removeUnattached=FALSE,...)

  DAVIDGODag(funChart, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
DAVIDGODag(funChart,
  ...)

Arguments

object

could be a character with the file name of the .tab report or data.frame already loaded.

fileName

character with the file name of the .tab report to load.

.Object

character to use in new function call. Possible values are: "DAVIDGenes", "DAVIDFunctionalAnnotationChart" or "DAVIDCluster".

Class

character to use in the as function call. Possible values are: "DAVIDGenes" and "DAVIDFunctionalAnnotationChart".

strict,ext

see as function.

funChart

DAVIDFunctionalAnnotationChart object.

type

character to indicate Gene Ontology main category: "BP", "MF" or "CC".

pvalueCutoff

numeric >0 <=1 to indicate the p-value to use as the threshold for enrichment. Default value is 0.1

removeUnattached

Should unattached nodes be removed from GO DAG? Default value is FALSE.

...

Additional parameters for lower level constructors (initialize).

Value

a DAVIDWebService object according to function call:

DAVIDGenes

object with genes description related data.

DAVIDFunctionalAnnotationChart

object with the respective report.

DAVIDFunctionalAnnotationTable

object with the respective report.

DAVIDCluster

Not possible to invoke as it is a Virtual class.

DAVIDGeneCluster

object with the respective report.

DAVIDTermCluster

object with the respective report.

DAVIDGODag

derived GOstats GO Direct Acyclic Graph from DAVIDFunctionalAnnotationChart data.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDFunctionalAnnotationChart: DAVIDFunctionalAnnotationChart-class, categories, categories, categories, ids, ids, ids, ids, ids, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Other DAVIDFunctionalAnnotationTable: DAVIDFunctionalAnnotationTable-class, categories, categories, categories, dictionary, dictionary, genes, genes, genes, genes, membership, membership, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D, subset, subset

Other DAVIDGODag: DAVIDGODag-class, benjaminis, benjaminis, bonferronis, bonferronis, counts, counts, fdrs, fdrs, foldEnrichments, foldEnrichments, listTotals, listTotals, percentages, percentages, popHits, popHits, popTotals, popTotals, summary, summary, summary, summary, terms, terms, universeCounts, universeMappedCount, upsideDown, upsideDown

Other DAVIDGeneCluster: DAVIDGeneCluster-class, genes, genes, genes, genes, ids, ids, ids, ids, ids, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Other DAVIDGenes: DAVIDGenes-class, genes, genes, genes, genes, ids, ids, ids, ids, ids

Other DAVIDTermCluster: DAVIDTermCluster-class, ids, ids, ids, ids, ids, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Examples

{
##DAVIDGenes example:
##Load Show Gene List file report for the input demo file 1, using data
##function. Then, create a DAVIDGenes object using the loaded data.frame
##geneList1.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)

##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/geneListReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidGenes1<-DAVIDGenes(untar(fileName,list=TRUE))


##DAVIDFunctionalAnnotationChart example
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
## object using the loaded data.frame funChart2.
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)

##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/functionalAnnotationChartReport2.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidFunChart2<-DAVIDFunctionalAnnotationChart(untar(fileName, list=TRUE))


##DAVIDFunctionalAnnotationTable example
##Load the Functional Annotation Table file report for the input demo
##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
##object using the loaded data.frame annotationTable1.
data(annotationTable1)
davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)

##In addition, the user can use the file name of the downloaded file report.
##Here, we need to first uncompressed the report included in the package, in
##order to load it.
setwd(tempdir())
fileName<-system.file("files/annotationTableReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidFunTable1<-DAVIDFunctionalAnnotationTable(untar(fileName, list=TRUE))


##Example DAVIDGODag
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDGODag object using
##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
##obtained from the loaded data.frame funChart2. In addition, we have
##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
##DAVID/GO.db database are not using the same version.
data(funChart2)
davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
pvalueCutoff=0.001, removeUnattached=TRUE)


##DAVIDGeneCluster example:
##Load the Gene Functional Classification Tool file report for the
##input demo list 1 file to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))


##DAVIDTermCluster example:
##Load the Gene Functional Classification Tool file report for the
##input demo file 2 to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/termClusterReport2.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RDAVIDWebService)
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GOstats
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand



Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: ggplot2

Attaching package: 'RDAVIDWebService'

The following object is masked from 'package:AnnotationDbi':

    species

The following object is masked from 'package:IRanges':

    members

The following objects are masked from 'package:BiocGenerics':

    counts, species

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RDAVIDWebService/DAVIDClasses-constructor.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DAVIDGenes
> ### Title: High level constructors for DAVIDWebService package's classes.
> ### Aliases: DAVIDFunctionalAnnotationChart,character-method
> ###   DAVIDFunctionalAnnotationChart,data.frame-method
> ###   DAVIDFunctionalAnnotationChart-methods
> ###   DAVIDFunctionalAnnotationTable,character-method
> ###   DAVIDFunctionalAnnotationTable,data.frame-method
> ###   DAVIDFunctionalAnnotationTable-methods
> ###   DAVIDGODag,DAVIDFunctionalAnnotationChart-method DAVIDGODag-methods
> ###   DAVIDGeneCluster,character-method DAVIDGeneCluster-methods
> ###   DAVIDGenes,character-method DAVIDGenes,data.frame-method
> ###   DAVIDGenes-methods DAVIDTermCluster,character-method
> ###   DAVIDTermCluster-methods initialize,DAVIDCluster-method
> ###   initialize,DAVIDFunctionalAnnotationChart-method
> ###   initialize,DAVIDFunctionalAnnotationTable-method
> ###   initialize,DAVIDGODag-method initialize,DAVIDGeneCluster-method
> ###   initialize,DAVIDGenes-method initialize,DAVIDTermCluster-method
> ###   DAVIDFunctionalAnnotationChart DAVIDFunctionalAnnotationTable
> ###   DAVIDGODag DAVIDGeneCluster DAVIDGenes DAVIDTermCluster as initialize
> 
> ### ** Examples
> 
> {
+ ##DAVIDGenes example:
+ ##Load Show Gene List file report for the input demo file 1, using data
+ ##function. Then, create a DAVIDGenes object using the loaded data.frame
+ ##geneList1.
+ data(geneList1)
+ davidGenes1<-DAVIDGenes(geneList1)
+ 
+ ##In addition, the user can use the file name of the downloaded file report.
+ ##Here, we need to first uncompressed the report included in the package, in
+ ##order to load it.
+ setwd(tempdir())
+ fileName<-system.file("files/geneListReport1.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidGenes1<-DAVIDGenes(untar(fileName,list=TRUE))
+ 
+ 
+ ##DAVIDFunctionalAnnotationChart example
+ ##Load the Functional Annotation Chart file report for the input demo
+ ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
+ ## object using the loaded data.frame funChart2.
+ data(funChart2)
+ davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)
+ 
+ ##In addition, the user can use the file name of the downloaded file report.
+ ##Here, we need to first uncompressed the report included in the package, in
+ ##order to load it.
+ setwd(tempdir())
+ fileName<-system.file("files/functionalAnnotationChartReport2.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidFunChart2<-DAVIDFunctionalAnnotationChart(untar(fileName, list=TRUE))
+ 
+ 
+ ##DAVIDFunctionalAnnotationTable example
+ ##Load the Functional Annotation Table file report for the input demo
+ ##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
+ ##object using the loaded data.frame annotationTable1.
+ data(annotationTable1)
+ davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)
+ 
+ ##In addition, the user can use the file name of the downloaded file report.
+ ##Here, we need to first uncompressed the report included in the package, in
+ ##order to load it.
+ setwd(tempdir())
+ fileName<-system.file("files/annotationTableReport1.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidFunTable1<-DAVIDFunctionalAnnotationTable(untar(fileName, list=TRUE))
+ 
+ 
+ ##Example DAVIDGODag
+ ##Load the Functional Annotation Chart file report for the input demo
+ ##file 2, using data function. Then, create a DAVIDGODag object using
+ ##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
+ ##obtained from the loaded data.frame funChart2. In addition, we have
+ ##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
+ ##DAVID/GO.db database are not using the same version.
+ data(funChart2)
+ davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
+ pvalueCutoff=0.001, removeUnattached=TRUE)
+ 
+ 
+ ##DAVIDGeneCluster example:
+ ##Load the Gene Functional Classification Tool file report for the
+ ##input demo list 1 file to create a DAVIDGeneCluster object.
+ setwd(tempdir())
+ fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))
+ 
+ 
+ ##DAVIDTermCluster example:
+ ##Load the Gene Functional Classification Tool file report for the
+ ##input demo file 2 to create a DAVIDGeneCluster object.
+ setwd(tempdir())
+ fileName<-system.file("files/termClusterReport2.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
+ }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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